Open
Conversation
adds registration of acquisition and atlases with smartem
![github-advanced-security[bot]](https://avatars.githubusercontent.com/in/57789?s=60&v=4){kind=small}
Codecov Report❌ Patch coverage is Additional details and impacted files@@ Coverage Diff @@
## main #748 +/- ##
==========================================
- Coverage 46.85% 46.81% -0.05%
==========================================
Files 91 91
Lines 9692 9756 +64
Branches 1278 1287 +9
==========================================
+ Hits 4541 4567 +26
- Misses 4929 4966 +37
- Partials 222 223 +1 🚀 New features to boost your workflow:
|
stephen-riggs
approved these changes
Feb 17, 2026
| atlas_registration_data: AtlasRegistration, | ||
| db=murfey_db, | ||
| ): | ||
| if SMARTEM_ACTIVE: |
Contributor
There was a problem hiding this comment.
Might be worth logging something here if smartem is not active
Contributor
There was a problem hiding this comment.
or if there is not a smartem_api_url
Contributor
Author
There was a problem hiding this comment.
I put some logs in
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
If installed and configured then starting a multigrid controller also adds an
Acquisitionin SmartEM and triggers the acquisition creation event.The atlas context is expanded to behave differently under different acquisition software. In the case that SerialEM is being used it will "register" atlases that it sees, meaning they will be registered with SmartEM if installed and configured. The SerialEM context is not accessed by discovery at the moment, as the others are, but is explicitly set in the API calls that trigger the multigrid controller setup. Note this means that this context will be used for all atlas analysers spawned by that controller.